feature_list.sgml

  <SECT1 ID="FEATURELIST">
    <TITLE>The Feature List</TITLE>
    <PARA>
The feature list is bit at the bottom of the main window of &art; (see <XREF
LINKEND="MAINWINDOW-OVERVIEW">). <![ %artemis-only; [ The feature list can be
toggled on and off from the display menu (see <XREF
LINKEND="DISPLAYMENU-SHOW-FEATURE-LIST">). ]]> The same component is used by
the two items in the view menus that show a sub-set of components (see <XREF
LINKEND="VIEWMENU-SHOW-CDS-GENES-PRODUCTS"> and <XREF
LINKEND="VIEWMENU-FEATURE-FILTERS">). The list contains information about each
feature in each active entry (see <XREF LINKEND="CONCEPTS-ACTIVEENTRY">), one
per line.
    </PARA>

    <PARA>
The lines show this information about the feature: the colour (see <XREF
LINKEND="CONCEPTS-COLOUR">), the key, start base, end base, the note field (if
any) and then the remaining qualifiers in EMBL/GENBANK format.  If the
correlation scores option is on then the scores will be shown just before the
note in each CDS line.
    </PARA>

    <SECT2 ID="FEATURELIST-SELECTION">
      <TITLE>Changing the Selection from the Feature List</TITLE>
      <PARA>
To select a feature from the list just click on it with the first mouse
button.  This will unselect anything that is currently selected.  To add a
feature to the selection rather than replacing the current selection, hold the
<LITERAL>shift</LITERAL> key while clicking.  A single feature can be removed
from the selection in the same way, because shift-clicking acts as a toggle.
      </PARA>
      <PARA>
See <XREF LINKEND="CONCEPTS-SELECTION"> for more about the selection.
      </PARA>
    </SECT2>

    <SECT2 ID="FEATURELIST-OTHERMOUSE">
      <TITLE>Other Mouse Controlled Functions</TITLE>
      <PARA>
Double clicking on a feature with the first mouse button causes both views and
the feature list to centre themselves on that feature.
      </PARA>
      <PARA>
A double click of the middle mouse button on a feature will open an edit
window for that feature.  This is the same as clicking once and then choosing
the Edit Selected Features menu item (see <XREF
LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
      </PARA>
    </SECT2>

    <SECT2 ID="FEATURELIST-POPUPMENU">
      <TITLE>The Pop-up Menu</TITLE>
      <PARA>
The pop-up menu is activated by pressing the third mouse button (see <XREF
LINKEND="MOUSEBUTTONS">) anywhere on the feature list.  The menu contains
shortcuts to some of the main window menus and three toggle buttons:
      </PARA>

      <SECT3>
        <TITLE>Save List to File</TITLE>
        <PARA>
Save the list of features to a file.
        </PARA>
      </SECT3>

      <SECT3>
        <TITLE>Show Selected Qualifier</TITLE>
        <PARA>
A qualifier can be selected to be displayed in the feature list.
        </PARA>
      </SECT3>


      <SECT3>
        <TITLE>Show Correlation Scores</TITLE>
        <PARA>
If this toggle is on the correlation scores for each feature will be show
between the end base and the note.
        </PARA>
      </SECT3>

      <SECT3>
        <TITLE>Show Gene Names</TITLE>
        <PARA>
This button controls whether the key or gene name is shown for each feature.
The "gene name" is actually the <LITERAL>/label</LITERAL> qualifier of the
feature.  If there is no <LITERAL>/label</LITERAL> then the
<LITERAL>/gene</LITERAL> qualifier is used.  If neither of the qualifiers
exists then the key is used.
        </PARA>
      </SECT3>

      <SECT3>
        <TITLE>Show Qualifiers</TITLE>
        <PARA>
If this option is on the feature qualifiers will be displayed after the note.
        </PARA>
      </SECT3>

      <SECT3>
        <TITLE>Show Product</TITLE>
        <PARA>
This button controls whether the <LITERAL>/note</LITERAL> or
<LITERAL>/product</LITERAL> is shown for each feature.  [default:
<LITERAL>/note</LITERAL> ]
        </PARA>
      </SECT3>

    </SECT2>
    <SECT2 ID="FEATURELIST-SCROLLING">
      <TITLE>Scrolling The List</TITLE>
      <PARA>
The scrollbar on the right of the list controls which part of the list of
active features is visible.  The list will also move if the user double clicks
on a feature in overview or DNA view areas, in which case the list will scroll
to that feature.
      </PARA>
    </SECT2>
  </SECT1>